The decision to expel former archbishop Francisco Jose Cox Huneeus and former bishop Marco Antonio Ordenes Fernandez — the latest heads to roll in a country hit hard by the cleric abuse scandal — could not be appealed, it said.
Both were stripped of their priesthood “as a consequence of overt acts of abuse against minors”.
The announcement came a day after the pope accepted the resignation of Washington DC archbishop Donald Wuerl, who has been blamed for not doing enough to deal with paedophile priests.
Saturday's defrocking was “an extremely unusual, if not unprecedented” move, said Ines San Martin, a Vatican expert writing in the Crux specialist Catholic website.
Defrocking is considered the harshest penalty for priests within the Church and means the offender is forbidden from exercising any clerical duties at all, even in private.
Scores of new cases of priestly sexual abuse of minors have come to light in Chile, deepening a crisis in the Roman Catholic church that has also embroiled Pope Francis.
On Saturday, Francis met with Chilean President Sebastian Pinera at the Vatican for talks on the “difficult situation” in Chile.
They discussed “the painful scourge of abuse of minors, reiterating the effort of all in collaboration to combat and prevent the perpetration of such crimes and their concealment”, the Vatican said.
The leaders “shared the hope that the church could live a true rebirth,” Pinera said in a statement.
A total of 167 bishops, priests and lay members of the church are now under investigation for sexual crimes committed in the South American country since 1960.
Fernandez became a bishop at the age of 42 in 2006, but resigned just six years later, allegedly for health reasons.
It later transpired that he had been accused of sexual abuse, sparking both a church and a civil investigation.
“The civil investigation is still ongoing because he's never responded to a court subpoena to give testimony,” Vatican expert San Martin said.
Fernandez was last seen in public in 2013 and had reportedly been living a life of penitence and prayer in Peru, she said.
Cox has long been the object of abuse allegations dating back to the 1970s.The Vatican on Saturday said he would remain a part of the institute of the Schoenstatt Fathers in Germany.
The prelate, now 85 and reportedly in precarious health, has resided in the institute since 2002, San Martin said.
Pope Francis has already apologised repeatedly to Chileans over the scandal, admitting the church failed “to listen and react” to the allegations, but vowed to “restore justice”.
In May, the Argentine pontiff accepted the resignation of five Chilean bishops amid accusations of abuse and related coverups.
Francis himself became mired in the scandal when, during a trip to Chile in January, he defended 61-year-old bishop Juan Barros, who was accused of covering up abuse by paedophile priest Fernando Karadima in the 1980s and 1990s.
Karadima was suspended for life by the Vatican over the allegations of child molestation.
Francis eventually accepted he was wrong to defend Barros and subsequently accepted his resignation.